Are you using the "Internal" or "Browser" Mode ? If your remote works in MP it sould also work with the "Internal" mode. (Need to set playback to "flash mode" on the amazon page and set the playback mode to "internal" on the onlinevideos site settings for amazon prime de).
Please make sure you have updated the site dll to the latest version (automatic site updates).

The "Browser" mode for amazon prime is not actively maintained and provided "as-is" so if there are any bugs/errors with this mode i'm not actively doing any work on this.

I'm only supporting the "Internal" mode, where the video stream is directly played back by Mediaportal